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Laonastes aenigmamus (Khanyou) is a recently described rodent species living in geographically separated limestone formations of the Khammuan Province in Lao PDR. Chromosomes of 21 specimens of L. aenigmamus were studied using chromosome banding as well as fluorescent in situ hybridization (FISH) techniques using human painting, telomere repeats, and 28S rDNA probes. Four different karyotypes were established. Study with human chromosome paints and FISH revealed that four large chromosomes were formed by multiple common tandem fusions, with persistence of some interstitial telomeres. The rearrangements separating the different karyotypes (I to IV) were also reconstructed. Various combinations of Robertsonian translocations or tandem fusions involving the same chromosomes differentiate these karyotypes. These rearrangements create a strong gametic barrier, which isolates specimens with karyotype II from the others. C-banding and FISH with telomere repeats also exhibit large and systematized differences between karyotype II and others. These data indicate an ancient reproductive separation and suggest that Laonastes is not a mono-specific genus. [ABSTRACT FROM AUTHOR]

Congenital tufting enteropathy (CTE) is a rare and severe enteropathy recently ascribed to mutations in the epcam gene. Here we establish SPINT2, previously ascribed to congenital sodium diarrhea, as a second gene associated with CTE and report molecular and immunohistochemistry data in 57 CTE patients. Inclusion criteria were early onset diarrhea and intestinal insufficiency with the typical histological CTE abnormalities. The clinical phenotype was registered, the entire coding regions of epcam and SPINT2 sequenced, and immunostaining of EpCAM and SPINT2 performed on intestinal biopsies. An epcam mutation was involved in 41 patients (73 %) who mainly displayed isolated digestive symptoms. Mutations severely affected gene expression since the EpCAM signal on intestinal tissues was either undetectable or low and irregular. Twelve other patients (21 %) carried mutations in SPINT2, and were phenotypically characterized by systematic association with keratitis ( p < 10) and, for half of them, with choanal atresia ( p < 10). Dependency on parenteral nutrition (PN) was comparable in patients with epcam or SPINT2 mutations, but the frequent epcam mutation c.556-14A>G (abnormal splicing) was significantly associated with a better outcome ( p = 0.032) with milder PN dependency to weaning in some cases. Finally, four patients (7 %) with isolated digestive symptoms had no detectable epcam or SPINT2 mutation. Two candidate genes, Elf3 and Claudin7, were excluded from this population. Our study allows us to separate CTE patients into at least three genetic classes, each with specific phenotypes. The genetics approach raises the question of the distinction between two congenital enteropathies. Our findings should help improve the diagnosis of CTE, guide toward strategies of long-term PN management, and limit indications for intestinal transplantation to life-threatening PN complications. [ABSTRACT FROM AUTHOR]

The Laotian rock rat ( Laonastes aenigmamus) is the single surviving member of the family Diatomyidae, which has a distribution restricted to the karstic region of Lao-PDR. Here we describe the development of 12 polymorphic microsatellites markers for the endangered Laotian rock rat using 454-sequencing. We successfully tested 12 markers in 30 individuals from 2 populations. Eleven of the 12 loci were polymorphic and the number of alleles detected per locus ranged from 2 to 11. Three of these loci deviated significantly from Hardy-Weinberg equilibrium, which coincides with the detection of possible null alleles. These microsatellite markers are expected to contribute in future research and conservation of L. aenigmamus. [ABSTRACT FROM AUTHOR]

In order to evaluate the circulation of hantaviruses present in southeast Asia, a large scale survey of small mammal species was carried out at seven main sites in the region (Cambodia, Lao People's Democratic Republic, and Thailand). Small scale opportunistic trapping was also performed at an eighth site (Cambodia). Using a standard IFA test, IgG antibodies reacting to Hantaan virus antigens were detected at six sites. Antibody prevalence at each site varied from 0 to 5.6% with antibodies detected in several rodent species ( Bandicota indica, B. savilei, Maxomys surifer, Mus caroli, M. cookii, Rattus exulans, R. nitidius, R. norvegicus, and R. tanezumi). When site seroprevalence was compared with site species richness, seropositive animals were found more frequently at sites with lower species richness. In order to confirm which hantavirus species were present, a subset of samples was also subjected to RT-PCR. Hantaviral RNA was detected at a single site from each country. Sequencing confirmed the presence of two hantavirus species, Thailand and Seoul viruses, including one sample (from Lao PDR) representing a highly divergent strain of Seoul virus. This is the first molecular evidence of hantavirus in Lao PDR and the first reported L segment sequence data for Thailand virus. [ABSTRACT FROM AUTHOR]

OBJECTIVES:Early onset inflammatory bowel diseases (EO-IBD) developing during the first year of life are likely to reflect inherited defects in key mechanism(s) controlling intestinal homeostasis, as recently suggested for interleukin 10 (IL10). Thus, we aimed to further elaborate the hypothesis of defective anti-inflammatory responses in patients with IBD.METHODS:The capacities of transforming growth factor β (TGFβ) and IL10 to inhibit proinflammatory cytokine production by monocyte-derived dendritic cells (MoDC) or peripheral blood cells (PBMC) was analyzed in 75 children with IBD, including 13 infants with EO-IBD (in whom autoimmune diseases or classical immunodeficiencies were ruled out). IL10 receptor-A/-B expression, STAT3 activation in response to IL6, IL10, IL21, IL22 were analyzed by FACS and western blotting. IL10RA and B genes were sequenced. The response to IL22 was tested in ileal/colonic tissue cultures. Tissue gene expression was analyzed by Taqman real-time polymerase chain reaction.RESULTS:Production of IL10 in response to bacterial motifs was normal in all IBD patients. In contrast to our original hypothesis, no defect of the anti-inflammatory potential of TGFβ and IL10 was observed in children with IBD or EO-IBD except two infants who presented with granuloma-positive colitis at 3 months of life: no response to IL10 was observed secondary to mutations in the α (p.R262C) or β (p.E141X) chain of IL10R, respectively, although a fully functional Jak-STAT3 pathway was present in both patients. When analyzing the regulation of intestinal bacterial clearance, we detected a defect in the patient with absent IL10 RB to upregulate protective transcripts in response to IL22, whereas all other EO-IBD patients, including the patient with an abnormal α chain, responded normally.CONCLUSIONS:Impaired IL10 signaling characterizes a subgroup of IBD patients, whereas the majority of children with severe IBD including EO forms normally produces and responds to IL10. Defective IL22 signaling may additionally impair intestinal epithelial clearance. Our data point out the complexity of IBD, which represent a group of distinct diseases with several pathogenetic abnormalities. [ABSTRACT FROM AUTHOR]

Background: Because Mycobacterium avium subspecies paratuberculosis (MAP), the etiologic agent of Johne's disease in ruminant, has been identified in the mucosal layer and deeper bowel wall in CD patients, the seroactivity against MAP may define a distinct subset of patients requiring individual treatment. The aim of this study was to assess the performance of anti-MAP antibodies in the diagnostic strategy for CD.Methods: Two hundred seventy-two individuals were included: 81 with CD, 36 with ulcerative colitis, 35 with coeliac diseases and 120 healthy blood donors. Anti-MAP were detected by ELISA using a purified protein derivative from MAP. Anti-Saccharomyces cerevisiae antibodies (ASCA) were detected by indirect immunofluorescence.Results: The sensitivity and specificity of anti-MAP and ASCA for CD diagnosis were similar (sensitivity: 0.33 ± 0.10 and 0.31 ± 0.10; specificity: 0.96 ± 0.03 and 0.98 ± 0.02, respectively). A combination of these two tests enabled an increase in sensitivity (0.53 ± 0.10), although specificity remained unchanged (0.95 ± 0.04). No correlation was found between anti-MAP positivity and clinical features such as age at onset and the duration of CD, disease location, or intestinal complications. Conversely, extra-intestinal manifestations of CD were statistically associated with a positivity of anti-MAP (48% vs. 24%, P = 0.028), mostly with respect to arthritis (44.5% vs. 13%, P < 0.002). Interestingly, anti-MAP and ASCA were also found in an active form of coeliac disease.Conclusion: Our results suggest a complementary role of ASCA and anti-MAP for CD diagnosis and a possible common role of bacteria in small intestinal mucosal damage in CD and coeliac disease. [ABSTRACT FROM AUTHOR]

Inflammatory bowel diseases (IBDs), including Crohn disease (CD) and ulcerative colitis (UC), often affect children and adolescents. Their diagnosis is based on the integration of clinical, biological, endoscopic, histological and radiological data. The paediatric radiologist may help the clinician in many ways. In children presenting with symptoms compatible with IBD, gut exploration by US may identify those who will benefit from more invasive explorations including endoscopy. During the process of diagnosis, small bowel exploration has a crucial role in differentiating CD from UC and in classifying the disease into subphenotypes. Finally, new imaging methods are useful during patient follow-up for assessing disease activity and for the diagnosis of complications. [ABSTRACT FROM AUTHOR]

Estimation of genotype-specific risks at a disease susceptibility locus is an important question that is best carried out in a prospective study. Nevertheless it is usually desirable to make use of data from the families that have already been collected to identify the susceptibility locus. Assuming that the families have been collected without regard to genotype at the locus in question, most of the information can be extracted by writing the likelihood in terms of the risk for a genotype relative to the standard genotype and conditional on the parental mating type. Parameters may then be estimated by explicit solution of likelihood equations. This method permits estimation of risks for heterozygotes and homozygotes for different alleles, testing of different modes of inheritance and heterogeneity of risk between alleles. It is applicable to risk alleles for any disease locus or incompletely penetrant phenotype. We have used the method to estimate risks of Crohn disease for different CARD/NOD2 15 mutations, using the families originally collected to identify this susceptibility locus. The odds ratio of Crohn disease were, respectively, 1.97±0.85, 3.05±* and 4.55±1.34 for the R702W, G9068R and 1007fs heterozygotes and 3.29±0.64, 12.13±* and 34.66±12.87 for the corresponding homozygotes. (* Signifies insufficient data to estimate these values.) These results confirm the dosage effect for CARD15/NOD2 mutations and demonstrate that the disease risks are very different in homozygotes. This last observation illustrates the power of this approach, especially for alleles with low or moderate frequency in the general population.European Journal of Human Genetics (2007) 15, 864–871; doi:10.1038/sj.ejhg.5201839; published online 25 April 2007 [ABSTRACT FROM AUTHOR]

BACKGROUND: Crohn's disease (CD) has been associated with CARD15/NOD2 mutations in Caucasians. The R702W, G908R, and 1007fs mutations represent 82% of the mutated chromosomes. The relative risk of developing CD in homozygous or compound heterozygous people has been estimated as between 10 and 40 times that of the general population. This high risk may support the opinion that CARD15/NOD2 variants are strong CD risk factors at the individual and population levels. SUBJECTS AND METHODS: The allele and genotype frequencies were calculated for the R702W, G908R, and 1007fs mutations in 3,575 Caucasian healthy controls recruited by 15 groups distributed on three continents. Geographic homogeneity was tested and the observed proportion of double mutants was compared with the expected value using χ2 tests. RESULTS: The allele frequencies of the R702W, G908R, and 1007fs mutations were 4.3% (3.6–4.9), 1.2% (0.8–1.6), and 2.3% (1.8–2.8), respectively, with large geographic fluctuations of the G908R, 1007fs, and wild-type alleles ( P < 0.0001). At the population level, no simple relationship was observed between mutation frequencies and the disease incidences in the studied populations. At the individual level, no significant deficit of double-dose mutation carriers among healthy controls was found, providing strong evidence that the penetrances of the most at-risk genotypes are low. CONCLUSION: Altogether, these data confirm that CARD15/NOD2 acts in interaction with other unknown risk cofactors. [ABSTRACT FROM AUTHOR]

Tracheal cytotoxin (TCT) was originally described as the minimal effector that was able to reproduce the cytotoxic response of Bordetella pertussis on ciliated epithelial cells. This molecule triggers pleiotropic effects such as immune stimulation or slow-wave sleep modulation. Further characterization identified TCT as a specific diaminopimelic acid (DAP)-containing muropeptide, GlcNAc-(anhydro)MurNAc-L-Ala-D-Glu-mesoDAP-D-Ala. Here, we show that the biological activity of TCT depends on Nod1, an intracellular sensor of bacterial peptidoglycan. However, Nod1-dependent detection of TCT was found to be host specific, as human Nod1 (hNod1) poorly detected TCT, whereas mouse Nod1 (mNod1) did so efficiently. More generally, hNod1 required a tripeptide (L-Ala-D-Glu-mesoDAP) for efficient sensing of peptidoglycan, whereas mNod1 detected a tetrapeptide structure (L-Ala-D-Glu-mesoDAP-D-Ala). In murine macrophages, TCT stimulated cytokine secretion and NO production through Nod1. Finally, in vivo, injection of the tetrapeptide structure in mice triggered a transient yet strong release of cytokines into the bloodstream and the maturation of macrophages, in a Nod1-dependent manner. This study thereby identifies Nod1 as the long sought after sensor of TCT in mammals. [ABSTRACT FROM AUTHOR]

Multiple factors are incriminated in the etiopathogeny of necrotizing enterocolitis (NEC) in premature infants, including oral feeding, vascular abnormalities, increase in pro-inflammatory cytokines, and inappropriate response of the intestinal barrier to bacterial microflora. CARD15/NOD2 is a gene recently recognized as important in the innate response to gut flora and is involved in Crohn's disease susceptibility. We thus tested its putative role in NEC. Ten children (seven boys and three girls) suffering from NEC who were admitted to Robert Debré hospital between 1999 and 2002 were retrospectively included in the study. Genetic screening of the 11 constant exons and the exon-intron junctions of CARD15/NOD2 by direct sequencing revealed no novel mutations of that gene in NEC patients. Furthermore, the three main mutations of CARD15/NOD2 (R702W, G908R, and 1007fs) associated with susceptibility to Crohn's disease were not found in these patients. Our results suggest that CARD15/NOD2 does not play a major role in genetic susceptibility to NEC. [ABSTRACT FROM AUTHOR]

Crohn's disease (CD) is a heterogeneous disorder. A genetic linkage to chromosome 16 (IBD1) has been previously observed and replicated in unrelated populations. Recently, in this region, NOD2/CARD15 has been identified as a susceptibility gene. The aim of this report is to determine whether this gene is implicated in CD in a Tunisian population. One hundred thirty patients with CD and 90 healthy individuals were genotyped for the three common NOD2 variants (C2104T in exon 4, G2722C in exon 8, and 3020insC in exon 11). Furthermore, the 11 exons of the NOD2 gene were sequenced in 20 patients with CD. Results showed that the frequency of the CARD15 variants in the Tunisian population is significantly lower than that observed in the European and American population. Direct sequencing of CARD15 did not permit us to identify a characteristic mutation in our population. No association was confirmed between CD and the NOD2 gene in our Tunisian population. Furthermore, the NOD2/CARD15 gene has a variable association with CD in different populations. These results indicate the genetic variation of CD in different ethnic groups. [ABSTRACT FROM AUTHOR]

Crohn's disease (CD) is a complex genetic disorder for which aetiology is unknown. Recently, genetic factors for susceptibility have been described. Several genetic loci have been mapped and partially explain the familial aggregations of the disease. However, environmental factors may also contribute to these aggregations. We considered that if the role of non-genetic factors was negligible, CD patients would be randomly distributed in sibships with multiple affected siblings. On the other hand if there was a significant environmental contribution, the siblings would be affected non-randomly over exposure status. In order to test this hypothesis, we studied 102 sibships with two or more affected siblings. A statistical test, named Cluster of Affected Sibling Test or CAST, was developed, based on the exact calculation of the probability of observing a given number of clusters of affected siblings in multiplex families. The null hypothesis of a random distribution of affected siblings was rejected (P=0,005). The observed excess of affected sibling clusters indicates that birth order influences the disease status. Considering that an adjacent order of birth is a global estimate of environmental sharing, this observation strongly suggests that environmental factors contribute to the observed familial aggregations of the disease. This observation provides evidence that familial CD is a relevant tool for further studies of environmental factors and gene-environment interaction. More generally, the CAST statistics may be widely applicable to estimate the involvement of environmental factors in the aetiology of other binary traits which may be observed in multiple members of the same sibship. [ABSTRACT FROM AUTHOR]

Crohn's disease (CD) is a complex genetic disorder for which a susceptibility gene, IBD1, has been mapped within the pericentromeric region of chromosome 16. In order to refine the location of IBD1, 77 multiplex CD families were genotyped for 26 microsatellite markers evenly spaced by approximately 1 cM. Nonparametric linkage analyses exhibited a maximum NPL score of 3.49 (P=2.37×10-4) in a region centred by markers D16S3136, D16S3117 and D16S770. Simulation studies showed that the probability for IBD1 to be located in a 5 cM region around these markers was 70%. A 2.5 Mb YAC and BAC contig map spanning this genetic region on chromosome band 16q12 was built. TDT analyses demonstrated suggestive association between the 207 bp allele of D16S3136 (P<0.05) and a new biallellic marker hb27g11f-end (P=0.01). These markers were located in the hb27g11 and hb87b10 BAC clones from the contig. Taken together, the present results provide a crucial preliminary step before an exhaustive linkage disequilibrium mapping of putatively transcribed regions to identify IBD1. European Journal of Human Genetics (2001) 9, 731–742. [ABSTRACT FROM AUTHOR]

Presents a study on the association of NOD2 leucine-rich repeat variants with susceptibility to Crohn's disease, a chronic inflammatory bowel disease. Prevalence of the disease; Information on single-nucleotide polymorphisms; Findings.

Studying the diversification of body size in a taxon of parasites allows comparison of patterns of variation observed in the parasites with patterns found in free-living organisms. The distributions of body size of oxyurid nematodes (obligate parasites of vertebrates and invertebrates) are lognormally right-skewed, except for male oxyurids in invertebrates which show left-skewed distributions. In these parasitic forms, speciose genera do not have the smallest body sizes. Parasite body size is positively correlated with host body size, the largest hosts possessing the largest parasites. This trend is shown to occur within one monophyletic group of oxyurids, those of Old World primates. Comparative methods are used to take account of the effects of phylogeny. The use of multiple linear regression on distance matrices allows measurements of the contribution of phylogeny to the evolution of body size of parasites. Evolution of body size in female pinworms of Old World primates appears to be dependent only on the body size of their hosts. The tendency of parasite body size to increase with host body size is discussed in the light of the evolution of life-history traits. [ABSTRACT FROM AUTHOR]

Presents data which supports the idea that some of the genetic factors in Crohn's disease (CD) may also contribute susceptiblity to ulcerative colitis. Ulcerative colitis and CD as sharing the same ethnic predisposition. The common occurrences of families containing some members with CD and some with ulcerative colitis; The degree to which locus on chromosome 16 leads to susceptibility.

Crohn Disease (CD) is a complex genetic disorder for which more than 140 genes have been identified using genome wide association studies (GWAS). However, the genetic architecture of the trait remains largely unknown. The recent development of machine learning (ML) approaches incited us to apply them to classify healthy and diseased people according to their genomic information. The Immunochip dataset containing 18,227 CD patients and 34,050 healthy controls enrolled and genotyped by the international Inflammatory Bowel Disease genetic consortium (IIBDGC) has been re-analyzed using a set of ML methods: penalized logistic regression (LR), gradient boosted trees (GBT) and artificial neural networks (NN). The main score used to compare the methods was the Area Under the ROC Curve (AUC) statistics. The impact of quality control (QC), imputing and coding methods on LR results showed that QC methods and imputation of missing genotypes may artificially increase the scores. At the opposite, neither the patient/control ratio nor marker preselection or coding strategies significantly affected the results. LR methods, including Lasso, Ridge and ElasticNet provided similar results with a maximum AUC of 0.80. GBT methods like XGBoost, LightGBM and CatBoost, together with dense NN with one or more hidden layers, provided similar AUC values, suggesting limited epistatic effects in the genetic architecture of the trait. ML methods detected near all the genetic variants previously identified by GWAS among the best predictors plus additional predictors with lower effects. The robustness and complementarity of the different methods are also studied. Compared to LR, non-linear models such as GBT or NN may provide robust complementary approaches to identify and classify genetic markers. [ABSTRACT FROM AUTHOR]

We have identified three missense mutations in the nucleotide-binding domain (NBD) of CARD15/NOD2 in four French and German families with Blau syndrome. Our findings indicate that, in addition to Crohn disease, CARD15 is involved in the susceptibility to a second granulomatous disorder. [ABSTRACT FROM AUTHOR]

Complex diseases involve both a genetic component and a response to environmental factors or lifestyle changes. Recently, genome-wide association studies (GWAS) have succeeded in identifying hundreds of polymorphisms that are statistically associated with complex diseases. However, the association is usually weak and none of the associated allelic forms is either necessary or sufficient for the disease occurrence. We argue that this promotes a network view, centred on functional redundancy. We adapted reliability theory to the concerned sub-network, modelled as a parallel array of functional modules. In our model, as long as one module remains active, the function correlated with the respective disease is ensured and disease does not occur. Genetic factors reduce the initial number of available modules while environment, contingent surroundings, personal history, epigenetics, and some intrinsic stochasticity influence their persistence time. This model reproduces age-specific incidence curves and explains the influence of environmental changes. It offers a new paradigm, according to which disease occurs due to a lack of functional elements, depending on many idiosyncratic factors. Genetic risk assessed from GWAS is only a statistical notion with no direct interpretation at the individual level. However, genomic profiling could be useful at population level in devising models to guide decisions in heakh care policy. [ABSTRACT FROM AUTHOR]